Abstract
BackgroundCo-expressing genes tend to cluster in eukaryotic genomes. This paper analyzes correlation between the proximity of eukaryotic genes and their transcriptional expression pattern in the zebrafish (Danio rerio) genome using available microarray data and gene annotation.ResultsThe analyses show that neighbouring genes are significantly coexpressed in the zebrafish genome, and the coexpression level is influenced by the intergenic distance and transcription orientation. This fact is further supported by examining the coexpression level of genes within positional clusters in the neighbourhood model. There is a positive correlation between gene coexpression and positional clustering in the zebrafish genome.ConclusionThe study provides another piece of evidence for the hypothesis that coexpressed genes do cluster in the eukaryotic genomes.
Highlights
Co-expressing genes tend to cluster in eukaryotic genomes
These mentioned studies on the coexpression of proximate genes and positional clustering of coexpressed genes are based on expression data obtained from biotechnologies such as Serial Analysis of Gene Expression (SAGE) data, DNA microarray, together with gene annotations
Proximate genes are coexpressed in the zebrafish genome In order to study the coexpression of proximate genes, we analyzed 100 expression datasets derived from Affymetrix microarray experiments
Summary
Co-expressing genes tend to cluster in eukaryotic genomes. This paper analyzes correlation between the proximity of eukaryotic genes and their transcriptional expression pattern in the zebrafish (Danio rerio) genome using available microarray data and gene annotation. Positional clustering of genes that are highly expressed in a specific tissue or a pathway has been revealed in different genomes [16,17,18,19]. These mentioned studies on the coexpression of proximate genes and positional clustering of coexpressed genes are based on expression data obtained from biotechnologies such as SAGE data, DNA microarray, together with gene annotations. There could be some selection force that keeps coregulated genes in the same region, for example, to make transcription more efficient as a group [10]
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